Variant report

Variant	rs1573815
Chromosome Location	chr3:52870132-52870133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11130331	0.82[JPT][hapmap]
rs1134546	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs11918800	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs11922961	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11922975	0.82[JPT][hapmap]
rs12488303	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12492391	0.95[JPT][hapmap]
rs12496077	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13083728	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001735	0.85[ASN][1000 genomes]
rs2071040	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071041	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071042	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2072391	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239547	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2240915	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2256332	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2276815	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2276817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276825	0.91[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336666	0.84[ASN][1000 genomes]
rs2336668	0.95[JPT][hapmap]
rs2336669	0.82[CEU][hapmap];0.82[GIH][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap]
rs2535633	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2564947	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2581780	0.82[CEU][hapmap]
rs2581801	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs2581810	0.82[CEU][hapmap]
rs2581815	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2878762	0.84[ASN][1000 genomes]
rs35004449	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3733047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755803	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821873	0.94[JPT][hapmap]
rs4302374	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4519686	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4687554	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687559	0.86[ASN][1000 genomes]
rs4687560	0.86[ASN][1000 genomes]
rs4687657	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687658	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687680	0.95[JPT][hapmap]
rs4687682	0.95[JPT][hapmap]
rs4687687	0.86[JPT][hapmap]
rs6445538	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445541	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6445547	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6445550	0.82[CEU][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap]
rs6768844	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs6769789	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6790314	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6792578	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs6795646	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs6797399	0.86[ASN][1000 genomes]
rs6798941	0.92[ASN][1000 genomes]
rs6803519	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs7620706	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626551	0.86[JPT][hapmap]
rs7638524	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7648514	0.82[CEU][hapmap]
rs9311485	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs9682464	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810807	0.95[JPT][hapmap]
rs9836499	0.95[JPT][hapmap]
rs9839035	0.86[ASN][1000 genomes]
rs9844736	0.82[CEU][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs9846976	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs9850563	0.95[JPT][hapmap]
rs9860296	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs9865094	0.86[CEU][hapmap]
rs9876403	0.87[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs9880978	0.95[JPT][hapmap]
rs9985365	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs1573815	ITIH4-AS1	cis	Artery Tibial	GTEx
rs1573815	TMEM110	cis	cerebellum	SCAN
rs1573815	GNL3	cis	cerebellum	SCAN
rs1573815	ITIH4-AS1	cis	lung	GTEx
rs1573815	SPCS1	cis	parietal	SCAN
rs1573815	GNL3	cis	parietal	SCAN
rs1573815	ITIH4	cis	parietal	SCAN
rs1573815	ITIH4	cis	Lymphoblastoid	GTEx
rs1573815	RBM6	cis	parietal	SCAN
rs1573815	GLT8D1	cis	lymphoblastoid	seeQTL
rs1573815	ITIH4-AS1	cis	Whole Blood	GTEx
rs1573815	MUSTN1	cis	Artery Aorta	GTEx
rs1573815	NEK4	cis	parietal	SCAN
rs1573815	TMEM110	cis	Muscle Skeletal	GTEx
rs1573815	ITIH4	cis	cerebellum	SCAN
rs1573815	ITIH4-AS1	cis	Artery Aorta	GTEx
rs1573815	ITIH4	cis	lymphoblastoid	seeQTL
rs1573815	ITIH4	cis	multi-tissue	Pritchard
rs1573815	RFT1	cis	cerebellum	SCAN
rs1573815	TMEM110	cis	parietal	SCAN
rs1573815	RBM6	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:52865600-52875200	Weak transcription	Dnd41	blood
9	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
10	chr3:52866000-52884800	Weak transcription	HMEC	breast
11	chr3:52866200-52870200	Weak transcription	Gastric	stomach
12	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
14	chr3:52866200-52885200	Weak transcription	NHEK	skin
15	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
16	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
18	chr3:52866600-52879200	Weak transcription	Osteobl	bone
19	chr3:52866800-52871000	Strong transcription	Spleen	Spleen
20	chr3:52866800-52872000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
23	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
24	chr3:52867000-52870600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:52867000-52871000	Strong transcription	Thymus	Thymus
26	chr3:52867000-52871200	Weak transcription	Pancreas	Pancrea
27	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:52867200-52871400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:52867600-52871800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:52867800-52870600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:52867800-52871200	Enhancers	Right Ventricle	heart
35	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:52868200-52870200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:52868400-52870200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:52868400-52870200	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:52868400-52871400	Enhancers	Fetal Heart	heart
41	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
42	chr3:52868600-52870400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:52868600-52870600	Strong transcription	Primary B cells from peripheral blood	blood
44	chr3:52868600-52872000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr3:52868600-52875200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:52868800-52870200	Enhancers	Colon Smooth Muscle	Colon
47	chr3:52868800-52870200	Enhancers	NHLF	lung
48	chr3:52868800-52870600	Strong transcription	Brain Substantia Nigra	brain
49	chr3:52868800-52873000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr3:52868800-52876800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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